Difference between revisions of "Manager Call 2020-06-17"

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(Noctua 2.0 rollout update)
(Bader gene sets)
 
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3) some of Bader gene sets could be of interest for QC ?
 
3) some of Bader gene sets could be of interest for QC ?
 
4) seems like GO should be providing gene sets derived from GO BP and GO MF (unsure about the use of GO CC but would be easy to generate too)
 
4) seems like GO should be providing gene sets derived from GO BP and GO MF (unsure about the use of GO CC but would be easy to generate too)
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One advantage is that the GO provides official releases. Can we provide files where we propagate annotations? Can we use external resource gene sets to cross check annotations? This would be very difficult.
  
 
==Noctua 2.0 rollout update==
 
==Noctua 2.0 rollout update==

Latest revision as of 09:01, 17 June 2020

Agenda

  • Agenda: Laurent-Philippe
  • Minutes: David
  • Present: David, Laurent-Philippe, Kimberly, Seth, Pascale, Suzi, Huiayu, PaulT, Chris
  • Regrets:Judy

Project plans for remainder of 2020

(Kimberly)

  • Make sure our priorities are clear for the remainder of the year
  • What are the most important things for the grant renewal?

We will do this next week.

Isoforms NOT in AmiGO/products

(Pascale, from feedback from Ruth) https://github.com/geneontology/go-site/issues/1105 Should they not be ?

I see them for mouse annotations. http://amigo.geneontology.org/amigo/search/annotation?q=*:*&fq=bioentity:%22MGI:MGI:1197518%22&sfq=document_category:%22annotation%22

We made the decision not to load the UniProt isoform annotation files. It is because the isoform gaf is not gene-centric. Some lines seem ok and some are not. Can we get a file that has the legitimate annotations? We will ask Alex for a file of the manually curated isoforms. Do we know how iften a GCRP identifier changes?

Evidence code for inferred annotations

(Pascale, from an ontology ticket) https://github.com/geneontology/go-ontology/issues/19461

Do we change the evidence code rule or do we change the evidence code? We have gone back and forth both ways. We will try to change the rule because it makes sense to traverse the ontology in the way we do for any other relationship. We will do this if the provenance is from GOC.

Bader gene sets

Approach to handle gene sets redundancy.

They are deriving gene sets for GO, but are using EBI and MGI for human and mouse annotations: http://baderlab.org/GeneSets#Sources.

Gene sets download: http://download.baderlab.org/EM_Genesets/current_release/Human/UniProt/

Proposals: 1) contact them to explain the benefits of fetching annotations from GOC instead of EBI/MGI instead of GOC 2) page on the go site to explain the above (differences & benefits from fetching annotations from GOC rather than a source; eg check, validations, etc) 3) some of Bader gene sets could be of interest for QC ? 4) seems like GO should be providing gene sets derived from GO BP and GO MF (unsure about the use of GO CC but would be easy to generate too)


One advantage is that the GO provides official releases. Can we provide files where we propagate annotations? Can we use external resource gene sets to cross check annotations? This would be very difficult.

Noctua 2.0 rollout update

  • Out on Monday and getting positive feedback
  • Some issues with rollout (dev/prod?); we will be following up

As we went ahead with the roll out, there has been good feedback.

Updated GO managers page to match the Project Org chart

(Pascale)